Contents iii

Prefacexv

Overview xv

Online XtalView Documentation xv

Conventions xvi

Fonts xvi
Mouse Buttons xvi
Terminology and Notation xvi

Introduction 1-1

What is XtalView? 1-1

What Systems Does XtalView Run On? 1-1
What Doesn't XtalView Do? 1-1
To Obtain XtalView 1-2

Getting Started 2-1

Setting Up Your Environment 2-1

Using XtalView 3-1

Software Overview 3-1

XtalView Crystal Database 3-1
History Files 3-1
File Formats 3-1
Other File Formats Supported 3-3
Plotting 3-3

Using XView 3-4

X11 Features 3-4
Textpanes 3-4
Backgrounding 3-4
Input and Output Files 3-5
Too Many Windows? 3-5

Using XtalView Windows 3-5

Command and Menu Buttons 3-6
Text field 3-7
Numerical field 3-7
Slider field 3-8
Setting field 3-8
Check box 3-9
Triangle button 3-9
Closing Pop-up Windows 3-9

Programming XtalView 4-1

Adding a Program to XtalView 4-1

Using the XtalView Database in Other Programs 4-1

Fortran Routines (lib/f77subs.c): 4-2
C Functions in crystlib.a 4-5

Window-based Applications 5-1

xtalview

a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model

• xcontur - a page-based contouring program for crystallographic maps
• xdf - disk full meter
• xedh - electron density histogram plotter
• xfft - calculate an electron density map or a Patterson function map by the Fast Fourier Transform method
• xfit - map fitting and molecular modeling program to display or manipulate models and fit to electron density
• xheavy - refine heavy atom derivatives and calculate phases.
• xhercules - searches for heavy atom sites.
• xmerge - merge and scale two data files.
• xmergephs - merge fin and phase files; phase derivatives and mutants
• xpatpred - predict Patterson peaks from a list of sites.
• xprepfin - prepare fin files.
• xresflt - resolution filter
• xrspace - reciprocal space viewer
• xskel - performs skeletonization on an electron density map
• xstat - analyze statistics on .fin, .df, or .phs files
• xtalmgr - manage XtalView projects and applications

Nonwindow-based Applications 6-1

• colorbyB - prepare a vu file from a PDB file colored by B-value
• cvtpdb - converts a pdb file between Cartesian and fractional coordinates, vice-versa, and coordinate transformations.
• cvtvu - convert a vu file between Cartesian and fractional coordinates
• cvtxyz - convert x,y,z between Cartesian and fractional coordinates
• deh - remove hydrogens from a pdb file.
• dumpphasit - reformat phasit format output files to XtalView
• deriv - calculate the derivative of a difference map at each atom
• grinchbones - convert a GRINCH ASCII format file to a vu file
• hercules - searches for heavy atom sites. This is a brute force application of Patterson correlation methods. It is slow, but extremely robust.
• matrices - dump the XtalView Cartesian/fractional conversion matrices
• mkskel - performs skeletonization on an electron density map (mkskel is part of the University of North Carolina GRINCH skeletonizat ion package).
• mu2fin - convert a XENGEN mulist file to an XtalView.fin file
• pdbfit - align two PDB objects using rotation and translation
• rescalc - calculates resolution of an index for the crystal in the CRYSTAL environment variable.
• resflt - resolution filter
• stfact - calculate structure factors from a PDB file.
• urf2xfit - convert an XENGEN urefls file to a vu file for display in xfit
• volume - calculates and displays the volume of a crystal unit cell
• xplortophs - reformat XPLOR phase files